biogems.info

New: CloudBioLinux packages are now listed on biogems.info !

#	biogem	description	by	version	released	stars	issues	total	90d*)	7d	90d**)
								downloads		commits
1	bio	Bioinformatics library (...)	BioRuby project	1.4.3	9 months	30	14	40445	3895	2	74
2	biodiversity	Parser of scientific names (...)	Dmitry Mozzherin	3.0.1	1 week		...	20690	1918	4	37
3	bio gem	Biogem is a software generator for Ruby in (...)	Raoul J.P. Bonnal, Pjotr Prins	1.3.4	13 months		...	18135	1811	0	18
4	bio samtools	Binder of samtools for Ruby, on the top (...)	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	0.6.0	5 months	13	3	14027	1517	0	0
5	entrez	Http requests to entrez e-utilities (...)	Jared Ning	0.5.8.1	21 months	4	...	11998	1155	0	0
6	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome (...)	Hiroyuki Mishima, Jan Aerts	0.5.2	5 months	11	1	10350	1102	0	24
7	bio gff3	Gff3 parser for big data (...)	Pjotr Prins	0.9.1	9 months		...	9645	891	0	0
8	intermine	Webservice client library for intermine data-warehouses (...)	Alex Kalderimis	1.01.00	11 weeks			9584	1055
9	sequenceserver	Blast search made easy! (...)	Anurag Priyam, Ben J Woodcroft, Yannick Wurm	0.8.5	3 weeks		...	8019	1123	0	17
10	bio logger	Log4r wrapper with extra features for roles and (...)	Pjotr Prins	1.0.1	13 months		...	7396	539	0	0
11	bio maf	Maf parser for BioRuby (...)	Clayton Wheeler	1.0.1	9 months	9	29	6507	1117	0	0
12	bio blastxmlparser	Very fast blast xml parser and library for (...)	Pjotr Prins	1.1.1	3 months	10	...	5234	551	1	1
13	bio grid	A biogem to submit jobs on a queue (...)	Francesco Strozzi	0.3.3	6 months		...	5103	1026	0	0
14	bio faster	A fast parser for fastq files (...)	Francesco Strozzi	0.4.5	11 months		...	4860	629	0	0
15	bio phyta	Pipeline to remove contaminations from est libraries (...)	Philipp Comans	0.9.4	17 months		...	4859	425	0	0
16	bio gadget	Gadgets for bioinformatics (...)	Shintaro Katayama	0.4.6	2 weeks		...	4708	2127	0	10
17	bio alignment	Support for multiple sequence alignments (msa) (...)	Pjotr Prins	0.0.7	11 months		...	4624	553	0	1
18	bio assembly	BioRuby assembly plugin (...)	Chase Miller, Francesco Strozzi	0.1.0	2 years	4	...	4389	366	0	0
19	genfrag	This is a development release (...)	Pjotr Prins and Trevor Wennblom	0.0.0.4	3 years			4368	292
20	scaffolder	Genome scaffolding for human beings (...)	Michael Barton	0.4.4	21 months		...	4291	346
21	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha (...)	George Githinji	0.7.1	2 months		...	4109	539	6	14
22	bio graphics	Library for visualizing genomic regions (...)	Jan Aerts	1.4	5 years			4078	276
23	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org) (...)	Rutger Vos, Anurag Priyam	1.1.0	12 months		...	3987	344	0	0
24	bio bigbio	Low memory sequence emitters (...)	Pjotr Prins	0.1.5	2 weeks		...	3838	448	0	21
25	eutils	Lightweight Ruby api for ncbi eutils (...)	Joon Lee, aka seouri	0.2.0	2 years	5	...	3751	302	0	0
26	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point (...)	George Githinji, Pascal Betz	0.1.3	14 months		...	3709	363	0	0
27	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps (...)	Hiroyuki Mishima	0.1.2	2 years	3	...	3555	312	0	0
28	bio signalp	A wrapper for the signal peptide prediction algorith (...)	Ben J Woodcroft	0.3.0	9 months		...	3502	428	0	0
29	bio octopus	Running and parsing of the protein transmembrane domain (...)	Ben J Woodcroft	0.1.1	2 years		...	3467	270	0	0
30	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv (...)	Pjotr Prins	0.8.0	6 months		...	3405	607
31	bio tm hmm	A BioRuby plugin for interaction with the transmembrane (...)	Ben J. Woodcroft	0.2.2	5 months		...	3384	425	0	0
32	bio ngs	Bio-ngs provides a framework for handling ngs data (...)	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	11 months	25	14	3380	300	8	11
33	goruby	Gene ontology (go) interface for Ruby (...)	Ben J Woodcroft	0.2.0	2 years		...	3164	218	0	0
34	bio svgenes	Create pretty svg-format images of features, gene models (...)	Dan MacLean	0.3.2	5 weeks		...	3061	1108	0	19
35	bio sambamba	Ruby wrapper for sambamba tool (...)	Artem Tarasov	0.0.5	9 months		...	3057	444	0	0
36	ruby ensembl api	Api to ensembl databases (...)	Jan Aerts, Francesco Strozzi	1.0.1	2 years	30	4	2981	200	0	0
37	bio bwa	Ruby binding for bwa mapping software (...)	Francesco Strozzi	0.2.2	2 years		...	2706	261	0	0
38	bio lazyblastxml	A plugin that allows you to parse large (...)	robsyme	0.4.0	24 months		...	2577	260	0	0
39	bio pileup iterator	Iterate through a samtools pileup file (...)	Ben J. Woodcroft	0.0.4	6 months	1	...	2346	278	0	0
40	bio kb illumina	Geneexpression illuminahumanannotation (...)	Raoul J.P. Bonnal	0.1.0	2 years		...	2258	195	0	0
41	bio plasmoap	Implementation of the plasmoap algorithm (...)	Ben J Woodcroft	0.0.2	16 months	1	...	2230	176	0	0
42	bio kmer counter	A biogem for counting small kmers for fingerprinting (...)	Ben J Woodcroft	0.1.1	7 weeks	5	...	2191	490	0	3
43	bio bgzf	Reading/writing bgzf blocks (...)	Artem Tarasov, Clayton Wheeler	0.2.1	9 months	1	...	2077	357	0	0
44	bio rdf	Bioinformatics triple-store support (...)	Pjotr Prins	0.0.2	12 months		...	1893	182	0	0
45	bio affy	Parse affymetrix cel/cdf files (...)	Pjotr Prins	0.5.1	17 months	2	1	1828	201	0	0
46	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser, (...)	Raoul J.P. Bonnal	0.0.1	21 months	1	...	1726	168	0	0
47	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal (...)	Ben J. Woodcroft	0.3.0	12 months	1	...	1575	179	0	0
48	bio gff3 pltools	Ruby wrapper for the gff3-pltools (...)	Marjan Povolni	0.3.0	9 months			1553	270
49	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be (...)	Ben J Woodcroft	0.0.3	16 months		...	1517	159	0	0
50	bio chembl	Chembl rest api client, parser and container (...)	Mitsuteru Nakao	0.1.3	10 months		...	1515	245	0	0
51	bio gngm	Next-generation mapping of mutations (...)	Dan MacLean	0.2.1	5 months	1	...	1446	286
52	biointerchange	An open source framework for transforming heterogeneous data (...)	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	0.2.2	1 week		...	1425	575	5	43
53	bio cd hit report	Read and manipulate cd-hit clusters (...)	George Githinji	0.1.0	3 weeks		...	1414	378	0	28
54	bio ucsc util	Ruby binding to the ucsc kent utilities (...)	throwern	0.1.2	7 months		...	1411	272
55	bio tabix	Ruby binding for samtools tabix (...)	throwern	0.1.3	12 months		...	1245	178	0	0
56	bio hmmer model	Parse pfam hmm definition files (...)	Ben J. Woodcroft	0.0.2	12 months	1	...	1189	179	0	0
57	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns (...)	Trevor Wennblom	1.0.0	20 months		...	1179	87	0	0
58	dna sequence aligner	Does high pairwise alignment of sequencing reads with (...)	John T. Prince	0.0.2	3 years			1170	80
59	bio sge	BioRuby plugin for sun grid engine (...)	Toshiaki Katayama	0.0.0	2 years		...	1162	104	0	0
60	bio hello	Hello world plugin for the BioRuby (just for (...)	Toshiaki Katayama	0.0.0	2 years	3	...	1152	102	0	0
61	bio gag	Bio-gag is a biogem for detecting and correcting (...)	Ben J Woodcroft	0.1.0	6 months		...	1006	185	0	0
62	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of (...)	Ben J Woodcroft	0.1.0	2 years	1	...	942	100	0	0
63	bio core ext	BioRuby core ext: plugins which require external library (...)	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	21 months		...	888	94	0	0
64	bio data restriction enzyme	Restriction enzyme dataset (...)	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	20 months		...	866	91	0	0
65	bio biolinux	Meta package for biolinux distribution (...)	Raoul J.P. Bonnal	0.1.0	20 months		...	851	91	0	0
66	bio foo	One-line summary of your gem (...)	Toshiaki Katayama	0.0.0	18 months	1	...	845	91	0	0
67	bio ensembl	A Ruby api to the ensembl database (...)	Jan Aerts, Francesco Strozzi	1.1.0	17 months	3	...	831	93	0	0
68	bio dbsnp	Decoding the dbsnp bitfield (...)	Hiroyuki Mishima	0.1.1	18 months		...	824	91	0	0
69	bio phyloxml	Phyloxml plugin for BioRuby (...)	Diana Jaunzeikare, Clayton Wheeler	0.9.0	12 months		...	817	92
70	bio protparam	A protparam compatible utility for BioRuby (...)	hryk	0.2.0	4 months		...	802	200	0	0
71	bio aliphatic index	A simple biogem that allows computation of the (...)	Ben J Woodcroft	0.0.1	16 months	1	...	779	93	0	0
72	bio exportpred	Wrapper around the exportpred algorithm for predicting p (...)	Ben J Woodcroft	0.0.1	16 months	1	...	775	92	0	0
73	bio hydropathy	Hydropathy scale for BioRuby (...)	Ben J Woodcroft	0.0.1	16 months		...	764	94	0	0
74	intermine bio	Biological extensions for the intermine webservice client library (...)	Alex Kalderimis	0.98.1	21 months			760	72
75	bio unichem	BioRuby plugin for unichem rest web service (...)	Mitsuteru Nakao	0.3.0	3 months		...	660	318
76	bio hmmer3 report	Enables parsing of hmmer version 3 reports (...)	Christian Zmasek, Ben J Woodcroft	0.0.1	12 months		...	640	104	0	0
77	bio incanter	Build graph with jRuby (...)	Matteo Picciolini	0.1.0	9 months		...	539	100
78	bio krona	This biogem is built around krona, a flashy (...)	Ben J. Woodcroft	0.0.1	9 months	1	...	511	98	0	0
79	bio ipcress	A programmatic interface to the ipcress in-silico pcr (...)	Ben J Woodcroft	0.0.1	9 months	1	...	506	86	0	0
80	bio synreport	Reports whether a nucleotide change results in synonymous (...)	Dan MacLean	0.1.2	6 days		...	475	215	9	9
81	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata (...)	Ben J. Woodcroft	0.0.1	4 months		...	292	113
82	bio qtlHD	(...) pre		pre				242	19

*) gem downloads (total & last 90 days) from rubygems.org as of 2013-05-21
**) number of commits on GitHub (last 7 days & last 90 days)